comparison scanpy-neighbours.xml @ 28:6417cccad133 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty

27:a58d4166805b

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

Compute a neighborhood graph of observations (`pp.neighbors`)
=============================================================

The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
which also provides a method for estimating connectivities of data points -
the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`,
connectivities are computed according to Coifman et al (2005), in the adaption of
Haghverdi et al (2016).

@HELP@

28:6417cccad133

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

Compute a neighborhood graph of observations (`pp.neighbors`)
=============================================================

The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
which also provides a method for estimating connectivities of data points -
the connectivity of the manifold (`method=='umap'`). If `method=='Gaussian'`,
connectivities are computed according to Coifman et al (2005), in the adaption of
Haghverdi et al (2016).

@HELP@